Investigation of cooperative effect exhibited by purely C-H—O hydrogen bonded (H-bonded) networks in linear and cyclic clusters of (1,3-cyclohexanedione)n (n = 2 to 6) has been carried out using density functional theoretical calculations. Linear clusters were found to show anti-cooperative behavior, while the cyclic clusters showed positive cooperativity. H-bond strengths and binding energies per bimolecular interaction were found to decrease with increasing cluster size for the linear clusters whereas their cyclic counterparts showed opposite trends. The extent of cooperativity has been found to show monotonic behavior for both linear and cyclic clusters and was found to reach an asymptotic limit with increasing cluster size. Natural bond orbital (NBO) analysis and atoms in molecule (AIM) calculations were found to corroborate the obtained results.
Ferroptosis is a recently characterized form of regulated necrosis with the iron-dependent accumulation of (phospho)lipid hydroperoxides (LOOH). It has attracted considerable attention for its putative involvement in diverse pathophysiological processes, such as cardiovascular disease and neurodegeneration. Here we describe the discovery of tetrahydroquinoxaline, a novel scaffold of ferroptosis inhibitors based on quantum chemistry methods. Tetrahydroquinoxaline deviates showed very good inhibition of ferroptosis, while being non cytotoxic for human cancer cells. And, the advantage of them is their small molecular weight (MW. = 148 Da) that can be coupled with other drugs to form multi-target drugs to better meet the treatment of complicated diseases.
Li-rich layered Mn-based oxides (LMOs) have attracted much attention due to their potential in various applications as cathode materials with high energy density. However, these cathode materials still suffer from drawbacks such as poor rate capability and voltage decay which makes further investigation vital and rational. Herein, the doping strategy is employed to investigate the effect of TM = Ti, Cu, and Zn on Li2Mn0.5TM0.5O3 for improving electrochemical performances of Li2MnO3. The electrochemical properties such as voltage, electrical conductivity, safety, structural stability, and kinetics and mechanism of Li-ion diffusion are evaluated and compared. All doped cathodes decrease the voltage reduction and improve the electrical conductivity coefficient in comparison with LMO. Ti dopants exhibit the potential to increase the maximum voltage of LMO and structural stability. Doping Zn and Cu elements can delay the oxygen loss which leads to a higher life cycle and safety. Also, the substitution of Zn dopants decreases the energy barrier against Li-ion diffusion and consequently, the lower Li-ion diffusion coefficient is expected. Using Ti, Cu, and Zn with α = 0.5 in Li2Mn0.5TMαO3 may furthermore open a door for the synthesis of lithium-rich materials with enhanced performance.
Excitation energy transfer is a ubiquitous process of fundamental importance for understanding natural phenomena, such as photosynthesis, as well as advancing technologies ranging from photovoltaics to development of photosensitizers and fluorescent labels. This work provides an overview of recent advancements in excitation energy transfer modeling with the PyFREC software package. Computational methods currently implemented in PyFREC include molecular fragmentation techniques, as well as methods for electronic coupling computations, analysis of coupled electronic excited states, and quantum dynamics simulations. Advanced functionality and possible vectors for future development of the package are also explored.
The ligand-promoted palladium-catalyzed hydroarylation of alkynes with arenes without directing group is able to furnish alkenyl chlorides via a 1,4-chlorine migration or trisubstituted alkenes. This reaction is challenging due to bidentate N, N ligand and electron-neutral arenes have rarely been reported to afford good yields. We carried out density functional theory calculations to better understand the elementary steps of the reaction and unveil the ligand effects and origin of substituent-controlled chemoselectivity of challenging C-H activation. For the n-propyl-substituted substrate, CMD process is the rate-determining step of the catalytic reaction. And the chemoselectivity is controlled by oxidative addition with the C-Cl bond cleavage and protonation process. However, for the reaction with 3,5-dimethylphenyl-substituented substrate, the key step of the whole catalytic cycle is the protonation process. The stronger electrostatic attractions, repulsive force and aryl substituent effects result in reverse chemoselectivity. Bidentate ligand L1 (2-OH-1,10-phenanthroline) reacts with Pd(OAc)2 to form a most stable square-planer species, which is different from the one formed by ligand L2(1,10-phenanthroline). The steric repulsion are found to be mainly responsible for no product with L2 as the ligand, which is different from as proviously reported.
The structure of transition state is very significant to further understand the related reaction system auxiliary N–N bond cleavage process. Here, in order to sort out some DFT functionals in searching the transition states in a N–N bond cleavage reaction mediated by the diiron complexes, compare the 45 density functionals with benchmark data of MP2 and DLPNO-CCSD(T) methods. By analyzing the structures and relative energies, we have found that four HGGA functionals (B1B95, mPW1PBE, HSE1PBE, HSEh1PBE) are the more consistently reliable methods. And the B1B95 functionals provide the most reliable energetic properties within 3 kcal/mol of the data of DLPNO-CCSD(T) method.
For the past decades, experiment like photoelectron spectroscopy and computational studies have demonstrated that highly coordinated transition metal centered boron nanoclusters favor planar or quasi-planar type structures, which could be potential building blocks for designing better nanostructure with tailored properties. In this paper, we have studied geometrical structures, electronic, optical and magnetic properties of the gas-phase Zn centered small boron clusters (n = 6–8) by employing density functional theory (DFT) and time dependent (TD) DFT calculations with B3LYP hybrid exchange-correlation functional. Two global minimum structures containing pyramidal and bi-pyramidal shaped ZnBm and Zn2Bm clusters shows symmetrical cyclic motif. The adsorption energy, ionization potential and molecular orbital analysis revealed that Zn is chemically adsorbed on the boron clusters occupying the hollow site and inverse sandwich bi-pyramidal (Zn2Bm) clusters are relatively more stable compared to singly doped boron nanoclusters. Vibrational modes are calculated to validate the true minima nature of the optimize structures which possesses no imaginary frequencies. All the pyramidal and bi-pyramidal clusters are optically active and show blue shifts in our calculated absorption spectra. The DFT computations indicate spin polarization in the pristine B7 cluster which induces strong ferromagnetism in pristine and adsorbed B7 clusters.
Ab initio calculations on systems involving singlet molecular oxygen (O2 (1g)) are challenging due to signicant multi-reference character arising from the degeneracy of the HOMO and LUMO orbitals in singlet oxygen. Here we investigate the stragegy of bypassing singlet oxygen’s multi-reference character by simply adding the experimen- tally determined singlet/triplet splitting (22.5 kcal/mol) to the triplet ground state of molecular oxygen. This method is tested by calculating rate constants for the reac- tions of singlet molecular oxygen with furan, 2-methylfuran, 2,5-dimethylfuran, pyrrole, 2-methylpyrrole, 2,5-dimethylpyrrole, and cyclopentadiene. The calculated rate con- stants are within a factor of 15 compared to experimentally determined rate constants. The results show that energy renement at the CCSD(T)-F12 level of theory is cru- cial to achieving accurate results. The reasonable agreement with experimental values validates the bypassing approach which can be used for other systems involving the 1,4-cyclo-addition of singlet oxygen. 2
The Kirchhoff index and degree-Kirchhoff index have attracted extensive attentions due to their wide applications in physics and chemistry. These indices have been computed for many interesting graphs, such as linear polyomino chain, linear / Möbius / cylinder hexagonal chain, and linear octagonal chain. In the present paper, we consider Möbius octagonal chain (Mn) and cylinder octagonal chain (M’n). Explicit closed-form formulae of the Kirchhoff index and the number of spanning trees are obtained for Mn and M’n.
Hybrid density functionals have been regularly applied in state-of-the-art computational models for predicting reduction potentials. Benchmark calculations of the absolute reduction potential of ferricenium/ferrocene couple, the IUPAC-proposed reference in nonaqueous solution, include the B3LYP/6-31G(d)/LanL2TZf protocol. We used this procedure to calculate ionization energies and reduction potentials for a comprehensive set of ferrocene derivatives. The protocol works very well for a number of derivatives. However, a significant discrepancy (> 1 V) between experimental and calculated data was detected for selected cases. Three variables were assessed to detect an origin of the observed failure: density functional, basis set, and solvation model. It comes out that the Hartree-Fock exchange fraction in hybrid-DFT methods is the main source of the error. The accidental errors were observed for other hybrid models like PBE0, BHandHLYP, and M06-2X. Therefore, hybrid DFT methods should be used with caution, or pure functionals (BLYP or M06L) may be used instead.
Hydrogen peroxide (H2O2), as clean oxidant, has long suffered from low efficiency and selectivity for the oxidation of olefins. In the present paper, the redox important ferrate anion (FeO42-) has been anchored into a silanol-decorated polyoxometalates (POM) to form single–site supported Fe-POM catalyst. And possible reaction mechanism for the epoxidation of propylene with hydrogen peroxide (H2O2) catalyzed by the Fe-POM catalyst have been investigated based on density functional theory with M06L functional. The study of molecular geometry, electronic structure, and bonding feature shows that the Fe-POM complex can be viewed as a high-valent Fe-oxo (Fe=O) species. The propylene molecule was activated by the Fe-POM catalyst via an effective electron transfer from propylene to the Fe-POM catalyst to form a cation propylene radical. Due to the high reactivity of radical species, the calculated activation energy barrier is only 4.50 kcal mol-1 for epoxidation of propylene to epoxypropane catalyzed by the Fe-POM catalyst. Subsequently, the calculated free energy profiles show that H2O2 was decomposed into a H2O molecule and a surface O species over the Fe-POM catalyst, and the remaining O atom attaches to the exposed the Fe center, resulting in the replenishing of Fe-POM catalyst via a two-state reaction pathway. The calculated activation energy barrier for this process is 23.42 kcal mol–1, and thus decomposition of H2O2 is the rate-determining step for the whole reaction. The Fe center serves as an electron acceptor, accepting electrons from the binding propylene molecule to form radical species in the first half of the reaction, and acts as the role of electron donor in the rest reaction steps to eliminate the radical feature, reduce the reactivity, and stop the reaction at the stage of the desired epoxypropane product.
The mechanisms of rhodium-catalyzed coupling reaction of ketoxime and 1,3-enynes were investigated by employing the density functional theory (DFT) calculations. Different 1,3-enynes would lead to different annulation products. Reaction A undergoes five sequential steps (C-H activation, 1,3-enyne migratory insertion, 1,4-Rh migration, cyclization, and deprotonation) to lead to [4 + 1] annulation product. Whereas, due to the electronic effect, the process generating [4 + 2] product in reaction A is restricted. In contrast, the electron-withdrawing group of N(Me)2 group in 1,3-enyne would bring about the [4 + 2] annulation product in reaction B. Our calculated results indicate that no [4 + 1] annulation product could be obtained in reaction C, in agreement with the experimental observation that the cis-allyl hydrogen in 1,3-enyne is crucial for the [4 + 1] annulation reaction.
Reactivity of thymine peroxy radical in DNA and its fate under hypoxia or oxygen-less conditions are studied at the M06-2X/6-31+G(d,p) level. The spaciously most accessible H2’ can be abstracted by C6-peroxy radical in an intranucleotidyl manner with the estimated barriers of 18.8 ~ 21.1 kcal/mol. The calculations show that C6-peroxy radical has a highly more reactivity towards C(sp3)-H abstraction reactions than its relative C6-yl, which is a counter-intuitive case. The formed hydroperoxide with the C6-OaObH2’ constituent can fast transfer ObH2’ group to C2’ radical in an intranucleotidyl manner with a low barrier (ca. 13.2 kcal/mol) and very strong heat release. The results show that the formed hydroperoxide product is unstable so that it could be quickly transformed into other species and thus is very hard to be experimentally observed. Afterwards, H2’ can be again abstracted by C6-oxyl radical to result in formation of thymine glycol which is the main products. The parallel C5-C6 bond scission reaction leads to formation of the precursor for 5-hydroxy-5-methylhydantion. The two competitive reactions have very low barriers. Based on our present calculations, the new radical reaction paths to formation of the DNA oxidation products are suggested under hypoxia or oxygen-less conditions, which is different from the previously suggested paths under high oxygen concentration surroundings.
There are views prevalent in the noncovalent chemistry literature that i) the O atom in molecules cannot form a chalcogen bond, and ii) if formed, this bond is very weak. We have shown here that these views are not necessarily true since the attractive energy between the oxygen atom of some molecules and several electron-rich anionic bases examined in a series of 34 ion-molecule complexes varied from the weak (ca –2.30 kcal mol-1) to the ultra-strong (–90.10 kcal mol-1). The [MP2 /aug-cc-pVTZ] binding energies for several of these complexes were found to be comparable to or significantly larger than that of the well-known hydrogen bond complex [FH···F]– (~ 40 kcal mol-1). The nature of the intermolecular interactions was examined using the quantum theory of atoms in molecules, second-order natural bond orbital and symmetric adaptive perturbation theory energy decomposition analyses. It was found that many of these interactions comprise mixed bonding character (ionic and covalent), especially manifest in the moderate to strongly bound complexes. All these can be explained by an n (lone-pair bonding orbital) -> σ* (anti-bonding orbital) donor-acceptor charge transfer delocalization. This study, therefore, demonstrates that the covalently bound oxygen atom in molecules can have a significant ability to act as an unusually strong chalcogen bond donor.
Based on the combination of novel carbon material graphynes (GYs) and superalkalis (OM3), a class of graphyne superalkali complexes, OM3+@(GY/GDY/GTY)– (M = Li, Na, and K), have been designed and investigated by density functional theory method. Computational results reveal that these complexes with high stability can be regarded as novel superalkali salts of graphynes due to electron transfer from OM3 to GYs. For second order nonlinear optical response, these superalkali salts exhibit large first hyperpolarizabilities (β0). Two important effects on β0 values are found, namely the atomic number of alkali atom in superalkali and the pore size of graphyne. Integrating the two effects, the selected combination of OLi3 with large pore size GTY can bring the considerable β0 value (6.5×105 au), which is a new record for superatom-doped graphynes. In the resulting complex, the OLi3 molecule is located at the center of the pore of GTY, forming a planar structure with the highest stability among these salts. Besides large β0 values, these superalkali salts of graphynes have deep-ultraviolet working region, hence can be considered as a new kind of high-performance deep-ultraviolet NLO molecules.
We systematically investigate the binding nature of CB towards 20 amino acids in both neutral (AAs) and protonated (AAs+) states by quantum chemistry methods. The result indicates molecular recognition process are enthalpy-driven. Among AAs, Arg and Asn shows the largest binding strength to CB, and for AAs+, Gln+ and Asn+ bind to CB the strongest. The binding strength of protonated CB/AA+ is much stronger than that of neutral CB/AA counterpart, due to the introduction of ion-dipole interaction and the increase number and strength of hydrogen bonds. Energy decomposition analysis (EDA) indicates that electrostatic interactions play major roles in both CB/AAs and CB/AAs+ complexes. Moreover, we analyzed the dependence of binding strength on single AA volume and dipole moment. This study is benefit for providing valuable information in predicting the recognition sites for sequence-based peptide or protein by CB and rationally designing synthetic host molecule for specific peptide or protein recognition.
Ternary metal hydrides play an essential role in the search for conventional high-temperature superconductors because they can be synthesized under mild condition and recovered at ambient pressure. It has been widely accepted that the electronic structure, metallization pressure and superconducting behavior of binary hydrides can be adjusted effectively by doping, replacing or introducing a new element. In this work, yttrium hydrides were chosen as parent hydrides while scandium was considered as the doped element to perform systematical crystal structure searches on the Sc-Y-H system under pressure. A new ternary hydride ScYH6 was found according to PSO calculations, and it presents high symmetric character below 150 GPa with a Pm-3 structure (cP8), then a P4/mmm phase (tP8) becomes favorable from 150 GPa. Importantly, cP8-ScYH6 is dynamically stable under pressure as low as 0.01 GPa with a Tc of 32.110 K for Coulomb pseudopotential μ∗=0.13, indicating ternary hydrides are promising candidates in the search for superconductors which can be synthesized under mild conditions in hydrogen-rich materials. The analysis through “triangle straight-line method” (TSLM) compared with enthalpy difference calculations showed the most reasonable synthesis pathway of ScYH6 is in the whole studied pressure range. The Tc of ScYH6 takes a linear relationship with pressure up to 52.907 K under 200 GPa. The lattice dynamical calculations demonstrate the H atoms in both cP8 and tP8 structures make crucial contributions to the superconducting behavior of ScYH6. These findings can further reveal the influence of doping, replacing and introducing new element on superconducting behavior of binary hydrides.
With the aim of describing bound and continuum states for diatomic molecules, we develop and implement a spectral method that makes use of Generalized Sturmian Functions (GSF) in prolate spheroidal coordinates. In order to master all computational issues, we apply here the method to one-electron molecular ions and compare it with benchmark data for both ground and excited states. We actually propose two different computational schemes to solve the two coupled differential equations. The first one is an iterative 1d procedure in which one solves alternately the angular and the radial equations, the latter yielding the state energy. The second, named direct $2d$ method, consists in representing the Hamiltonian matrix in a two–dimensional GSF basis set, and its further diagonalization. Both spectral schemes are timewise computationally efficient since the basis elements are such that no derivatives have to be calculated numerically. Moreover, very accurate results are obtained with minimal basis sets. This is related on one side to the use of the natural coordinate system and, on the other, to the intrinsic good property of all GSF basis elements that are constructed as to obey appropriate physical boundary conditions. The present implementation for bound states paves the way for the study of continuum states involved in ionization of one or two-electron diatomic targets.